1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 12

sp. nov., isolated from coastal surface water, and reclassification of as comb. nov. Free

Abstract

A novel Gram-stain-negative, aerobic, yellow-pigmented bacterium was isolated from seawater of Aoshan Bay, and designated as strain ASW18. Strain ASW18 was a long-rod-shaped bacterium without flagellum and lacked gliding ability. Based on 16S rRNA gene phylogeny, strain ASW18 showed the closest relationship to MCCC 1A06690, with a sequence similarity of 97.0 %. Strain ASW18 was able to grow at 25–40 °C, at pH 5.5–9.5 and with 0.5–9 % (w/v) NaCl. The genomic DNA G+C content of strain ASW18 was 37.3 %. The predominant cellular fatty acids of strain ASW18 were iso-C, iso-C 3-OH and iso-C G. The major polar lipids were phosphatidylethanolamine, phosphatidyldimethylethanolamine, an aminolipid and three unidentified lipids. The respiratory quinone of strain ASW18 was menaquinone with six isoprene units (MK-6). Based on the present polyphasic analysis, strain ASW18 represents a novel species of the genus , for which the name sp. nov. is proposed; the type strain is ASW18 (=MCCC 1K04203=KCTC 72852). In addition, it is also proposed that should be reclassified as comb. nov.; the type strain is CSW06 (=CGMCC 1.15761=JCM 31455=KCTC 52375=MCCC 1K03195).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Croceivirga litoralis sp. nov. , seawater and taxonomy
Funding
This study was supported by the:
  • Fundamental Research Funds of Shandong University (Award 2018TB012)
    • Principle Award Recipient: Jihua Liu
  • Joint Fund of National Natural Science Foundation of China (Award U1906216)
    • Principle Award Recipient: Jihua Liu
  • National Key Research and Development Program of China (Award 2019YFA0606704)
    • Principle Award Recipient: Jihua Liu
  • National Key Research and Development Program of China (Award 2016YFA0601103)
    • Principle Award Recipient: Jihua Liu
  • National Key Research and Development Program of China (Award 2017YFA0604300)
    • Principle Award Recipient: Jihua Liu
  • National Key Research and Development Program of China (Award 2018YFA0605800)
    • Principle Award Recipient: Jihua Liu
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004541
2020-11-03
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/12/6348.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004541&mimeType=html&fmt=ahah

References

  1. Hu D, Wang L, Chen Y, Li X, Du Y, Shao Z et al. Croceivirga radicis gen. nov., sp. nov., isolated from a rotten tropical mangrove root. Int J Syst Evol Microbiol 2017; 67:3733–3738 [View Article][PubMed]
     [Google Scholar]
  2. Lee H-S, Kwon KK, Yang S-H, Bae SS, Park CH et al. Description of Croceitalea gen. nov. in the family Flavobacteriaceae with two species, Croceitalea eckloniae sp. nov. and Croceitalea dokdonensis sp. nov., isolated from the rhizosphere of the marine alga Ecklonia kurome. Int J Syst Evol Microbiol 2008; 58:2505–2510 [View Article][PubMed]
     [Google Scholar]
  3. Sly LI, Taghavi M, Fegan M. Phylogenetic position of Chitinophaga pinensis in the Flexibacter-Bacteroides-Cytophaga phylum. Int J Syst Bacteriol 1999; 49 Pt 2:479–481 [View Article][PubMed]
     [Google Scholar]
  4. Ling S-K, Guo L-Y, Chen G-J, Du Z-J. Motilimonas eburnea gen. nov., sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2017; 67:306–310 [View Article][PubMed]
     [Google Scholar]
  5. Wang Y, Yang X, Liu J, Wu Y, Zhang X-H. Muricauda lutea sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:1064–1069 [View Article][PubMed]
     [Google Scholar]
  6. DeLong EF. Archaea in coastal marine environments. Proc Natl Acad Sci U S A 1992; 89:5685–5689 [View Article][PubMed]
     [Google Scholar]
  7. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  8. Hollingsworth PM, Ennos RA. Neighbour joining trees, dominant markers and population genetic structure. Heredity 2004; 92:490–498 [View Article][PubMed]
     [Google Scholar]
  9. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  11. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [View Article][PubMed]
     [Google Scholar]
  12. Kumar S, Stecher G, Tamura K, Sudhir K, Glen S. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  13. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  14. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG et al. Short protocols in molecular biology. A compendium of methods from current protocols in molecular biology. Gene 1995; 88:127–130 [View Article]
     [Google Scholar]
  15. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
     [Google Scholar]
  16. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  17. Medlar AJ, Törönen P, Holm L. AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 2018; 46:W479–W485 [View Article][PubMed]
     [Google Scholar]
  18. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article][PubMed]
     [Google Scholar]
  19. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Göker M et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes . Front Microbiol 2019; 10:10 [View Article][PubMed]
     [Google Scholar]
  20. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
     [Google Scholar]
  21. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
  22. Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M, Bel M. PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. Bioinformatics 2017; 33:2946–2947 [View Article][PubMed]
     [Google Scholar]
  23. Dong B, Zhu S, Chen T, Ren N, Chen X et al. Muricauda oceani sp. nov., isolated from the East Pacific Ocean. Int J Syst Evol Microbiol 2020; 70:3839–3844 [View Article][PubMed]
     [Google Scholar]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  25. Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP et al. Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. mBio 2014; 5:e02136–14 [View Article][PubMed]
     [Google Scholar]
  26. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. ASM Microbe Mag 2014; 9:111–118 [View Article]
     [Google Scholar]
  27. Bernardet J-F, Nakagawa Y, Holmes B. Subcommittee On The Taxonomy Of Flavobacterium And Cytophaga-Like Bacteria Of The International Committee On Systematics Of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
     [Google Scholar]
  28. Pan J, Sun C, Zhang X-Q, Huo Y-Y, Zhu X-F et al. Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment. Int J Syst Evol Microbiol 2014; 64:2512–2516 [View Article][PubMed]
     [Google Scholar]
  29. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007 pp 330–393
     [Google Scholar]
  30. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207 [View Article]
     [Google Scholar]
  31. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101 Newark, DE: MIDI Inc 1990. http://www.midi-inc.com
  32. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  33. BLIGH EG, DYER WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004541
Loading
Croceivirga litoralis sp. nov., isolated from coastal surface water, and reclassification of Muricauda lutea as Croceivirga lutea comb. nov.
Int J Syst Evol Microbiol 70, 6348 (2020); https://doi.org/10.1099/ijsem.0.004541
/content/journal/ijsem/10.1099/ijsem.0.004541
/content/journal/ijsem/10.1099/ijsem.0.004541
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error